Approximately 88% of the patients with clinically typical chronic myelogenous leukemia (CML) present with a cytogenetic abnormality known as the Philadelphia chromosome (Ph[unreadable]1[unreadable]). This chromosome aberration has also been reported at a much lower frequency in both acute lymphocytic leukemia (ALL) and acute myelogenous leukemia (AML). The occurrence of such a specific alteration suggests that there are selected genes expressed that are associated with this phenotypically distinct leukemic population. To investigate this possibility, poly(A[unreadable]+[unreadable])RNA from a patient with a 100% Ph[unreadable]1[unreadable]-positive CML in the chronic phase of disease was used for construction of a complementary DNA (cDNA) library. Recombinant clones representing moderately to abundantly transcribed sequences were selected by annealing [[unreadable]32[unreadable]P]-cDNA transcribed from homologous RNA and assessing radioactivity in the hybrids. Four hundred and seventeen colonies from an initial 729 (57.2%) displayed a hybridization signal more intense than controls, indicating these recombinant plasmids contained sequences homologous to moderately or highly expressed RNAs from the CML patient. Screening of these 417 clones utilizing probes derived from normal human placenta, acute myelomonocytic leukemia (AMML), and other CML samples was used to select clones likely to contain sequences highly represented in all CML cells. Sixteen recombinants were selected that repeatedly failed to display hybridization with the placenta and AMML-derived probes. Initial analysis of eight of the clones indicates that six contain sequences preferentially expressed in CML and various Ph[unreadable]1[unreadable]-positive acute leukemias. One clone, C-A3, has been studied with 63 different RNA samples. This sequence was found to be highly expressed in the chronic phase of both Ph[unreadable]1[unreadable]-positive and Ph[unreadable]1[unreadable]-negative CML as well as in Ph[unreadable]1[unreadable]-positive acute myelogenous leukemia (AML) and Ph[unreadable]1[unreadable]-positive acute lymphocytic leukemia (ALL). Expression was reduced in lymphoblastic crisis of CML and relatively absent in myeloblastic crisis of CML. While preliminary, the results suggest that this probe may be useful in aiding in the diagnosis of Ph[unreadable]1[unreadable]-negative CML and distinguishing Ph[unreadable]1[unreadable]-positive AML from myeloblastic crisis of CML. (G)